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PubMed1976

A comparison of the 16S ribosomal RNAs from mesophilic and thermophilic bacilli: some modifications in the Sanger method for RNA sequencing.

Two modifications in the Sanger two dimensional electrophoretic procedure for RNA analysis are reported. One increases resolution on the primary fingerprint to the point that digests of large RNAs, of the size 1500-3000 nucleotides yield well resolved fingerprint patterns. The other is a novel endonucleolytic procedure that proves useful in determining sequences of the large oligonucleotides produced by T1 ribonuclease. These modifications have been used in determining the catalogs of oligomers produced by T1 ribonuclease digestion of 16S rRNAs from three related organisms, Bacillus subtilis, B.pumilus and B.stearothermophilus. The possible effects of adaptation to a thermophilic niche on ribosomal RNA primary structure and the phylogenetic relatedness of the two mesophilic Bacilli are discussed.

Animals↗
PubMed1978

Ribosomal RNA homologies and the evolution of the filamentous blue-green bacteria.

Ribosomal RNA (rRNA) sequence homology (as determined by comparisons of T1 oligonucleotide catalogs of 32P-labeled 16S rRNAs) has been used to assess phylogenetic relationships within the filamentous and unicellular blue-green bacteria, and to identify regions of evolutionary conservatism within blue-green bacterial 16S rRNAs. Nostoc and Fishcherella, representatives of two morphologically distinct and highly differentiated orders, are shown to be as closely related (on the basis of RNA sequence homology) as typical members of the non-blue-green bacterial genus Bacillus. They are further shown to be (on the same basis) indistinguishable from typical unicellular members of a subgroup of the unicellular blue-green bacterial order Chroococcales. These results have general implications for studies of the origin of differentiated prokaryotes and of evolutionary change in prokaryotic macromolecules. In particular, they provide indirect evidence that the divergences of contemporary major prokaryotic groups are truly ancient ones.

Base Sequence↗
PubMed1978

Are extreme halophiles actually "bacteria"?

Comparative cataloging of the 16SrRNA of Halobacterium halobium indicates that the organism did not arise, as a halophilic adaptation, from some typical bacterium. Rather, H. halobium is a member of the Archaebacteria, an ancient group of organisms that are no more related to typical bacteria than they are to eucaryotes.

Base Sequence↗
PubMed1982

Taxonomic relations between archaebacteria including 6 novel genera examined by cross hybridization of DNAs and 16S rRNAs.

DNAs from 16 species of archaebacteria including 6 novel isolates were hybridized with 16S rRNAs from 7 species representing different orders or groups of the urkingdom of archaebacteria. The yields, normalized for the number of genes per microgram of DNA, and the temperature stabilities of all hybrids were determined and related to each other. A taxonomic tree constructed from such fractional stability data reveals the same major divisions as that derived from comparative cataloging of 16S rRNA sequences. The extreme halophiles appear however as a distinct order besides the three known divisions of methanogens. The methanogens, the halophiles and Thermoplasma form one of two clearly recognizable branches of the archaebacterial urkingdom. The order represented by Sulfolobus and the related novel order Thermoproteales form the other branch. Three novel genera, Thermoproteus, Desulfurococcus and the "stiff filaments" represent three families of this order. The extremely thermophilic methanogen Methanothermus fervidus belongs to the Methanobacteriales. SN1, a methanogen from Italy, appears as another species of the genus Methanococcus. Another novel methanogen, M3, represents a genus or family of the order Methanomicrobiales.

Archaea↗
PubMed1986

Immunogenetics.

The 1985 Catalog of Mapped Genes (Human Gene Mapping 8; 33) has been used to pick out the known, immunologically important genes; these are then discussed in the following order: genes controlling organs, tissues and cells of the immune apparatus, genes determining 'self' structures, genes determining the structures of immunological specificity, genes determining substances with immunoregulatory and effector properties. The symbols for the genes and the biological functions of their products are explained. The genetics of the ABO blood groups, of the HLA-system and of antibody formation are given in rather more detail.

ABO Blood-Group System↗
PubMed1983

The evolutionary pattern of aromatic amino acid biosynthesis and the emerging phylogeny of pseudomonad bacteria.

Pseudomonad bacteria are a phylogenetically diverse assemblage of species named within contemporary genera that include Pseudomonas, Xanthomonas and Alcaligenes. Thus far, five distinct rRNA homology groups (Groups I through V) have been established by oligonucleotide cataloging and by rRNA/DNA hybridization. A pattern of enzymic features of aromatic amino acid biosynthesis (enzymological patterning) is conserved at the level of rRNA homology, five distinct and unambiguous patterns therefore existing in correspondence with the rRNA homology groups. We sorted 87 pseudomonad strains into Groups (and Subgroups) by aromatic pathway patterning. The reliability of this methodology was tested in a blind study using coded cultures of diverse pseudomonad organisms provided by American type Culture Collection. Fourteen of 14 correct assignments were made at the Group level (the level of rRNA homology), and 12 of 14 correct assignments were made at the finer-tuned Subgroup levels. Many strains of unknown rRNA-homology affiliation had been placed into tentative rRNA groupings based upon enzymological patterning. Positive confirmation of such strains as members of the predicted rRNA homology groups was demonstrated by DNA/rRNA hybridization in nearly every case. It seems clear that the combination of these molecular approaches will make it feasible to deduce the evolution of biochemical-pathway construction and regulation in parallel with the emerging phylogenies of microbes housing these pathways.

Alcaligenes↗
PubMed1987

Structure of 5S rRNA in actinomycetes and relatives and evolution of eubacteria.

The primary structure of 5S ribosomal RNA has been determined in five species belonging to the genus Mycobacterium and in Micrococcus luteus. The sequences of 5S RNAs from Actinomycetes and relatives point to the existence in this taxon of a bulge on the helix that joins the termini of the molecule. An attempt was made to reconstruct bacterial evolution from a sequence dissimilarity matrix based on 142 eubacterial 5S RNA sequences and corrected for multiple mutation. The algorithm is based on weighted pairwise clustering, and incorporates a correction for divergent mutation rates, as derived by comparison of sequence dissimilarities with an external reference group of eukaryotic 5S RNAs. The resulting tree is compared with the eubacterial phylogeny built on 16S rRNA catalog comparison. The bacteria for which the 5S RNA sequence is known form a number of clusters also discernible in the 16S rRNA phylogeny. However, the branching pattern leading to these clusters shows some notable discrepancies with the aforementioned phylogeny.

Bacteria↗
PubMed1984

The case for a polyphyletic origin of mitochondria: morphological and molecular comparisons.

The comparative morphology and pigmentation of protists suggest that those with tubular mitochondrial cristae belong to a different lineage than those with lamellar cristae and that the evolutionary divergence might have been very early. We propose that the difference in cristal morphology is the result of separate origins of the mitochondria from endosymbionts related to the Rhodospirillaceae (purple nonsulfur bacteria) but differing in the morphology of their internal membranes. Comparisons of the cytochromes c of protists and the Rhodospirillaceae and of 16s rRNA T1 oligonucleotide catalogs in the Rhodospirillaceae do not contradict, and in fact provide support for, the idea. More extensive evidence may be lacking simply because cytochromes c have been studied in very few protists with tubular mitochondrial cristae.

Biological Evolution↗
PubMed1977

The evolution of a functional real-time laboratory records retrieval and archival system.

The vast flood of information resulting from medical record keeping in a clinical laboratory must be cataloged and archived. To deal with this problem we designed an approach employing automated report generation by a laboratory computer, data base management of patient laboratory results, and automated microform generation via computer output microform (COM). This paper documents the steps that led to the system we are currently employing. The system described maintains the availability of current patient laboratory data, creates a microform archive and an on-line index, and serves as the data base for research inquiries. In addition, we have experienced a cost savings over manual procedures and now possess the capability of expansion without the costly addition of personnel.

Archives↗
PubMed2001

Hemolymph analysis and evaluation of newly formulated media for culture of shrimp cells (Penaeus stylirostris).

Creation of a shrimp cell line has been an elusive goal. This failure may be due to the composition of the cell culture medium, which may be inadequate to support primary cultured cells. Shrimp hemolymph should contain the nutritional components needed to support cell growth and division. We report here the comprehensive biochemical analysis of hemolymph from the blue shrimp, Penaeus stylirostris (Litopenaeus stylirostris) (see Holthuis, L. B. Shrimps and prawns of the world, in: FAO species catalog. Vol. 1. Rome: Food and Agriculture Organization of the United Nations; 1980), for free amino acids (FAAs), carbohydrates, electrolytes, metals, pH, and osmolality. Levels of hemolymph components were compared to 2xL-15 with 20% fetal bovine serum, a commonly used culture medium for crustacean cells. The FAAs, taurine and proline, and the metals, strontium and zinc, were significantly higher in hemolymph than in the 2 x L-15 medium. In contrast, other FAAs were up to 50 times higher in the 2 x L-15 medium than in the hemolymph. To mimic more closely the hemolymph composition, we created two new media based on either the 0.2 x L-15 or the M199 medium. We compared the microscopic appearance of cells cultured in these media and evaluated deoxyribonucleic acid (DNA) and protein synthesis by 3H-thymidine uptake and 35S-methionine uptake assays. The ovary cells of P. stylirostris cultured in either of the new media formed monolayers, while the cells cultured in 2 x L-15 medium did not. Despite these differences, there was no evidence of sustained DNA or protein synthesis with any of the media. Future studies to establish a shrimp cell line should focus on analysis of the cell cycle and on overcoming the molecular blocks to cell division.

Animals↗
PubMed1989

Shifting ditypic site analysis: heuristics for expanding the phylogenetic range of nucleotide sequences in Sankoff analyses.

We describe and illustrate a simple heuristic approach to the Sankoff methods for construction of parsimonious evolutionary trees from nucleotide sequence data. The procedure is intended to permit more valid inferences, particularly from relatively short sequences, concerning relationships among taxa separated for long time intervals. The procedure is based on the great variability of evolutionary plasticity among sites in the molecules and removes from consideration the more highly variable sites. Editing is accomplished after classifying sites in carefully aligned arrays of sequences. Only "ditypic sites," i.e., sites observed in only two evolutionary states within the array, are used in making phylogenetic inferences. This strategy makes possible the construction of good approximations to the most parsimonious Steiner trees, by means of efficient programs that require "dense species arrays," i.e., species sets that differ from each other by relatively small numbers of differences in conservative sites. The technique is illustrated with 5S and 5.8S rRNA sequence data from published catalogs.

Base Sequence↗
PubMed1999

Interactive web-based radiology teaching file.

This multimedia radiology teaching file was developed for medical students, residents, physicians, and researchers to present teaching components related to clinical studies. Patient studies are used to create teaching cases, user can also create lecture series and custom presentations (catalogs) by linking related text and images. The user is able to make and preserve his/her own notes related to reviewed information. From the computer workstation, the user can perform search our case library by American College of Radiology (ACR) codes, keywords, modalities, or text. Results are presented in custom pages and include text lists, thumbnails lists, rescaled images, and full-size images. Text can be easily printed in custom format or exported to an ASCI file. To preserve the privacy of the student, access to our database is granted to the web browser by log-in panel. Image and text can be imported from Digital Imaging and Communications in Medicine (DICOM)-compatible devices or entered by using web forms. In conclusion, we developed a multifunctional interactive teaching environment accessible for multiplatform internet users.

Computer Security↗
PubMed2000

[Health care reform 2000--effects on inpatient care].

The health reform 2000 in Germany has little impact on the structural deficits of the German health service. The monopolies of hospitals for inpatient and of contract doctors for outpatient care are not changed. The budgeting of hospitals remains. In future there will be a catalog of operations that may only be carried out on an outpatient basis. The duty for quality assurance is specified and intensified. Implementation of innovative medical treatments in hospital will to be done only under strict control of a new countrywide committee. A new DRG-based price system for hospitals will be established.

Budgets↗
PubMed2006

[Survival strategy of burn centers in the context of the German DRG system: reimbursement].

BACKGROUND: The system of German diagnosis-related groups (G-DRG) has undergone modifications for burn cases (Y-DRG) since 2003. The DRG catalog includes two of seven Y-DRGs without a case weight. METHODS: The BG Trauma Center in Ludwigshafen could demonstrate that the cost of burn care treatment could not be reimbursed through Y-DRGs in 2004. RESULTS: By being accredited as a so-called "individual hospital-based unit" for burn care (Besondere Einrichtung), it was possible to agree to an "all-inclusive" contract. The daily rate is reimbursed with 2792 Euros/day. The reimbursement of the treatment of burn patients is thus cost covering. CONCLUSION: In summary the budget for 2006 should be calculated by an individualized hospital rate for all Y-DRGs, especially as it was shown that the additional payments (Zusatzentgelte) for selected therapies did not cover the costs of special treatments in burn care in 2005 and 2006. The problem has been recognized and published internationally. The special and cost-intensive treatment of burn patients is difficult to calculate in a system of diagnosis-related groups due to the low number of cases.

Budgets↗
PubMed2006

An updated 'Essex' by 'Forrest' linkage map and first composite interval map of QTL underlying six soybean traits.

DNA marker maps based on single populations are the basis for gene, loci and genomic analyses. Individual maps can be integrated to produce composite maps with higher marker densities if shared marker orders are consistent. However, estimates of marker order in composite maps must include sets of markers that were not polymorphic in multiple populations. Often some of the pooled markers were not codominant, or were not correctly scored. The soybean composite map was composed of data from five separate populations based on northern US germplasm but does not yet include 'Essex' by 'Forrest' recombinant inbred line (RIL) population (E x F) or any southern US soybean cultivars. The objectives were, to update the E x F map with codominant markers, to compare marker orders among this map, the Forrest physical map and the composite soybean map and to compare QTL identified by composite interval maps to the earlier interval maps. Two hundred and thirty seven markers were used to construct the core of the E x F map. The majority of marker orders were consistent between the maps. However, 19 putative marker inversions were detected on 12 of 20 linkage groups (LG). Eleven marker distance compressions were also found. The number of inverted markers ranged from 1 to 2 per LG. Thus, marker order inversions may be common in southern compared to northern US germplasm. A total of 61 QTL among 37 measures of six traits were detected by composite interval maps, interval maps and single point analysis. Seventeen of the QTL found in composite intervals had previously been detected among the 29 QTL found in simple interval maps. The genomic locations of the known QTL were more closely delimited. A genome sequencing project to compare Southern and Northern US soybean cultivars would catalog and delimit inverted regions and the associated QTL. Gene introgression in cultivar development programs would be accelerated.

Chromosome Mapping↗
PubMed2026

Genetic architecture and evolution of stripe rust resistance uncovered using diverse panels of wheat lines and North American Puccinia striiformis f. sp. tritici isolates.

Screening global wheat germplasm with a diverse collection of pathogen races expands the catalog of novel Yr loci and identifies new sources of broad-spectrum resistance against evolving Pst populations. Newly emerging highly virulent races of Puccinia striiformis f. sp. tritici (Pst) often defeat deployed resistance genes (Yr), highlighting the need for novel sources of durable resistance. A global diversity panel of 377 spring wheat (Triticum aestivum L.) lines was screened for all-stage resistance (ASR) against a panel of diverse 20 Pst isolates at the seedling stage and for adult-plant-stage resistance (APR) against natural mix of field races. Genome-wide association mapping identified 77 unique Yr loci. Of these, 34 overlapped with the previously mapped 1150 Yr loci, confirming the robustness of our GWAS results, while 43 were likely novel. Comparison of the nine adult-plant-stage Yr loci mapped in our study with known APR genes identified only one overlap, with Yr29. Except for Yr29, APR genes Yr18 and Yr36 were detected at low frequencies, indicating that resistance in our panel may arise from less characterized or novel sources. Two wheat lines, lacking widely effective Yr5 and Yr15 alleles, exhibited resistance to all 20 Pst races at the seedling stage and natural field races at the adult stage, suggesting that they may carry novel, broad-spectrum ASR alleles. Wheat improvement had no effect on the frequency of ASR alleles but resulted in a threefold increase in the frequency of APR alleles, suggesting that the latter were subjected to more consistent breeding selection over time. Our findings underscore the value of combined screening of diverse germplasm with diverse pathogen races to identify novel sources of broad-spectrum resistance for breeding stripe rust resistant cultivars.

Triticum↗
PubMed2001

Pharmacological studies of prepulse inhibition models of sensorimotor gating deficits in schizophrenia: a decade in review.

RATIONALE: Patients with schizophrenia exhibit deficits in an operational measure of sensorimotor gating: prepulse inhibition (PPI) of startle. Similar deficits in PPI are produced in rats by pharmacological or developmental manipulations. These experimentally induced PPI deficits in rats are clearly not animal models of schizophrenia per se, but appear to provide models of sensorimotor gating deficits in schizophrenia patients that have face, predictive, and construct validity. In rodents, disruptions in PPI of startle are produced by: stimulation of D2 dopamine (DA) receptors, produced by amphetamine or apomorphine; activation of serotonergic systems, produced by serotonin (5-HT) releasers or direct agonists at multiple serotonin receptors; and blockade of N-methyl-D-aspartate (NMDA) receptors, produced by drugs such as phencyclidine (PCP). Accordingly, dopaminergic, serotonergic, and glutamatergic models of disrupted PPI have evolved and have been applied to the identification of potential antipsychotic treatments. In addition, some developmental manipulations, such as isolation rearing, have provided non-pharmacological animal models of the PPI deficits seen in schizophrenia. OBJECTIVE: This review summarizes and evaluates studies assessing the effects of systemic drug administrations on PPI in rats. METHODS: Studies examining systemic drug effects on PPI in rats prior to January 15, 2001 were compiled and organized into six annotated appendices. Based on this catalog of studies, the specific advantages and disadvantages of each of the four main PPI models used in the study of antipsychotic drugs were critically evaluated. RESULTS: Despite some notable inconsistencies, the literature provides strong support for significant disruptions in PPI in rats produced by DA agonists, 5-HT2 agonists, NMDA antagonists, and isolation rearing. Each of these models exhibits sensitivity to at least some antipsychotic medications. While the PPI model based on the effects of direct DA agonists is the most well-validated for the identification of known antipsychotics, the isolation rearing model also appears to be sensitive to both typical and atypical antipsychotics. The 5-HT PPI model is less generally sensitive to antipsychotic medications, but can provide insight into the contribution of serotonergic systems to the actions of newer antipsychotics that act upon multiple receptors. The deficits in PPI produced by NMDA antagonists appear to be more sensitive to clozapine-like atypical antipsychotics than to typical antipsychotics. Hence, despite some exceptions to this generalization, the NMDA PPI model might aid in the identification of novel or atypical antipsychotic medications. CONCLUSIONS: Studies of drug effects on PPI in rats have generated four distinctive models that have utility in the identification of antipsychotic medications. Because each of these models has specific advantages and disadvantages, the choice of model to be used depends upon the question being addressed. This review should help to guide such decisions.

Animals↗
PubMed2003

All-terrain vehicle injuries in children: injury patterns and prognostic implications.

BACKGROUND: All-terrain vehicle (ATV) accidents are common in children. Our purpose was to identify imaging patterns associated with ATV injuries in children. PATIENTS AND METHODS: The study group comprised 141 consecutive children admitted to a tertiary pediatric hospital following ATV accidents. Medical records were evaluated for demographics and patient outcome. All imaging studies were reviewed and abnormalities cataloged. RESULTS: Extremity fractures were the most common injuries in our study, occurring in 38% of patients. Lower extremity fractures were more common than upper extremity fractures. Partial foot amputation, an unusual injury, was present in three children. Torso injuries were present in 22% of the children. Pulmonary contusions, but not abdominal injuries, were significantly associated with long-term disability or death (p=0.01). Brain injuries occurred in 19% of the children and were significantly associated with death or long-term disability (p=<0.001). No association of brain injury and skull fracture was present. CONCLUSIONS: A wide variety of injuries were identified in children with ATV accidents. Partial foot amputation, an unusual injury, was identified in three children. Brain injuries and lung contusions detected by computed tomography were associated with long-term disability and death. Radiologists need to be aware of injuries associated with ATV accidents.

Adolescent↗